I bought both a Black Mission and Magnolia fig tree in March of 2011, they were 4 inches tall single stalks.

We've repotted them a few times and now both are a foot and a half tall, The Black Mission is single trunk, about 3/8 inch thick, woody, and looks like what I believe a tree should look like. The Magnolia has 5 different skinny green 1/4 inch shoots growing all over the place with no prominent trunk. Both are in 1 gallons pots and have lots of leaves and seem healthy.

Do different fig varieties have different growing preferencs or is it random per tree? Like would one find 2 Black Missions where one is bushy and one tree shaped? 

Should I take off some of the skinny Magnolia trunks (and root em) in hopes that the remaining trunk thickens up or just leave it because that is what it wants to do natively?

The shape of the tree is dependent on how it is grown and how important ease of harvest is to you.

Trees grown in containers will naturally be smaller therefor they can be grown single trunk (some prefer that look). Those grown in-ground and subject to being freeze-killed should be grown in the open (multi-trunk. Up to 5) shape to increase survival of a trunk. Hope this helps!

I have noticed some tend to grow more bushy and some more upright.
The grower does have the last say however.

Martin is right. There are certainly some variants which have a tendency towards "weediness" and must be thinned out or they will become an impassable thicket making harvesting a chore and reducing fruiting buds towards the center.

I have two Magnolias that are multiple trunked but grow what I call 'short and wide'. Both are probably 20 years old or older, and neither are over 8' tall, and one is about 10' wide while the other I keep pruned to about 6' wide.

These will live in pots for the foreseeable future so I will keep the Magnolia down to 5 trunks so it doesn't become too bushy.